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SR-VP_0-2_scaffold_141_2072294_prodigal-single.1__X__X__00124

Bact-Vir

SR-VP_0-2_scaffold_141_2072294_prodigal-single.1__X__X__00124

Identity

Kingdom:
phage

Quality

77.9 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 4-62
PDB
Domain cluster: representative
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2fnaA02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.85 63.0 5.78e-01 89.8% 61.8%
3uk6A02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.77 61.0 5.51e-01 98.3% 62.7%
3bosA02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.77 62.0 5.98e-01 96.6% 79.1%
2z4sA02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.75 61.0 5.76e-01 98.3% 75.0%
2kebA00 1.10.8.530 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › DNA polymerase alpha-primase, subunit B, N-terminal domain 0.74 59.0 5.45e-01 98.3% 67.9%
2c9oB03 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.73 58.0 5.28e-01 96.6% 65.1%
3smvA02 1.10.150.750 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.70 55.0 5.06e-01 88.1% 80.5%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.69 49.0 4.72e-01 93.2% 67.2%
7y11B01 1.10.8.20 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p 0.69 55.0 5.47e-01 96.6% 84.1%
3vkhB07 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 52.0 3.58e-01 81.4% 30.7%
2xzmV01 1.10.60.20 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Ribosomal protein S17 0.68 43.0 4.28e-01 71.2% 62.3%
2k3nA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.67 59.0 4.33e-01 100.0% 73.1%
2cfoA04 1.10.8.70 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 0.66 51.0 5.24e-01 84.7% 92.6%
2h21A02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.65 46.0 3.30e-01 74.6% 59.4%
2kzcA00 1.10.790.20 Mainly Alpha › Orthogonal Bundle › Major Prion Protein › Domain of unknown function DUF1476 0.65 51.0 4.56e-01 88.1% 61.2%
3ilkA02 1.10.8.590 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.65 47.0 4.55e-01 79.7% 75.0%
1j09A04 1.10.8.70 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 0.64 46.0 4.92e-01 84.7% 97.9%
1zp2A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.64 52.0 4.30e-01 93.2% 59.8%
1hm7B00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.64 55.0 3.50e-01 100.0% 22.0%
1sz2A02 3.40.367.20 Alpha Beta › 3-Layer(aba) Sandwich › Hexokinase; domain 1 › 0.63 47.0 3.26e-01 79.7% 68.5%
3paoB00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.63 54.0 3.42e-01 98.3% 100.0%
2bnlC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 51.0 3.86e-01 88.1% 47.0%
2w00A02 3.90.640.50 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.62 50.0 4.71e-01 91.5% 87.7%
2uuzB00 1.10.10.2020 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Host-nuclease inhibitor protein Gam 0.62 45.0 4.04e-01 78.0% 85.9%
3mgdB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.61 50.0 3.76e-01 94.9% 90.1%
1ysyA00 1.10.8.370 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › nsp7 replicase 0.59 48.0 4.44e-01 100.0% 71.8%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.59 42.0 3.36e-01 74.6% 95.5%
2fe3B01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 44.0 3.93e-01 81.4% 81.2%
1vt0k00 1.10.3230.20 Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › P22 tail accessory factor (Gp4) 0.59 45.0 3.52e-01 88.1% 60.0%
2c9kA01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.58 50.0 3.35e-01 98.3% 66.1%
1jr8A00 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.58 48.0 4.00e-01 94.9% 51.4%
4etsA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 45.0 4.03e-01 86.4% 78.2%
1sxjD03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.58 45.0 3.97e-01 88.1% 61.5%
1iv8A04 1.10.10.470 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Maltooligosyl trehalose synthase; domain 4 0.58 47.0 4.01e-01 96.6% 54.6%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.57 48.0 4.40e-01 98.3% 75.3%
2hwjA02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.57 47.0 4.73e-01 96.6% 100.0%
4gxbA02 1.20.80.60 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.57 40.0 3.97e-01 81.4% 71.0%
3nz4B03 1.10.274.20 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3 0.56 49.0 4.10e-01 100.0% 66.3%
2mw2A00 1.20.1280.40 Mainly Alpha › Up-down Bundle › Monooxygenase › HHA 0.56 37.0 3.59e-01 71.2% 59.7%
3ckdA02 1.20.58.360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Shigella T3SS effector IpaH defines 0.56 45.0 3.73e-01 98.3% 64.5%
3nrkA01 1.10.4030.10 Mainly Alpha › Orthogonal Bundle › Triger factor/SurA peptide-binding fold › Porin chaperone SurA, peptide-binding domain 0.55 43.0 3.00e-01 86.4% 26.7%
3lfuA02 1.10.10.160 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.55 39.0 3.81e-01 79.7% 81.4%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.53 43.0 3.19e-01 96.6% 46.9%
5nl9A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.50 42.0 3.74e-01 93.2% 82.1%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3249392 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.83 69.0 6.68e-01 100.0% 81.5%
4341780 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.83 68.0 6.58e-01 96.6% 81.5%
4458447 148.1.3.21 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_4 0.81 66.0 6.24e-01 96.6% 75.7%
4121495 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.80 65.0 6.09e-01 98.3% 72.0%
3547029 148.1.3.221 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › NPHP3_hel 0.80 68.0 6.06e-01 96.6% 67.1%
5055046 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.78 65.0 6.53e-01 100.0% 91.7%
2819342 3788.1.1.1 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › VPR 0.77 63.0 6.16e-01 88.1% 84.4%
3254545 103.11.1.0 ↗ alpha arrays › RuvA-C › RMI1 N-terminal helical domain-related › RMI1 N-terminal helical domain-related 0.75 60.0 6.25e-01 96.6% 94.5%
5067754 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.74 61.0 6.27e-01 96.6% 98.2%
4517001 632.3.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.74 57.0 6.01e-01 91.5% 100.0%
3963295 148.1.3.238 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › DUF815 0.73 58.0 5.97e-01 89.8% 94.5%
4119015 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.73 60.0 6.06e-01 94.9% 90.0%
3738331 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.72 53.0 5.47e-01 81.4% 90.9%
3998578 142.1.1.41 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › RabGAP-TBC 0.72 57.0 5.61e-01 91.5% 96.9%
3508870 148.1.3.172 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_14 0.71 60.0 5.11e-01 96.6% 65.0%
3733392 101.1.2.166 ↗ alpha arrays › HTH › HTH › winged helix domain › MCM6_C 0.71 47.0 3.73e-01 72.9% 34.8%
5011924 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.71 62.0 4.28e-01 100.0% 38.0%
4024018 327.11.2.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_6 0.71 56.0 4.42e-01 89.8% 43.1%
3651890 604.1.1.3 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › MAP65_ASE1 0.70 61.0 4.32e-01 100.0% 35.7%
4059363 142.3.1.1 ↗ alpha complex topology › Sigma2 domain-like › Mitochondrial morphogenesis protein Sld7 C-terminal domain › Mitochondrial morphogenesis protein Sld7 C-terminal domain › Sld7_C 0.69 59.0 5.19e-01 98.3% 84.4%
3995291 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.69 56.0 5.48e-01 94.9% 87.7%
4453955 4230.1.1.3 ↗ alpha arrays › DnaD domain › DnaD domain › DnaD domain › DnaB_2 0.68 55.0 4.39e-01 91.5% 51.2%
4969033 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 44.0 3.10e-01 86.4% 21.7%
119186 592.4.1.1 ↗ alpha arrays › PWI domain-like › Repetitive domains of egg case silk protein TuSp1 › Repetitive domains of egg case silk protein TuSp1 › RP1-2 0.67 59.0 4.33e-01 100.0% 73.1%
3487282 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 46.0 3.14e-01 88.1% 20.0%
3469499 327.11.2.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_6 0.66 58.0 4.32e-01 100.0% 40.7%
3591437 601.29.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › TM1646-like › TM1646-like 0.65 51.0 4.27e-01 84.7% 57.0%
4169204 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.65 41.0 4.21e-01 74.6% 67.3%
3466259 3722.1.1.1 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › MAP65_ASE1 0.64 56.0 3.47e-01 100.0% 18.1%
3589739 101.1.4.3 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3 0.63 51.0 4.14e-01 96.6% 44.0%
4050022 101.35.1.4 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.62 41.0 4.28e-01 72.9% 72.7%
3383371 3722.1.1.1 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › MAP65_ASE1 0.62 54.0 3.37e-01 96.6% 18.1%
3697477 7581.1.1.7 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › Ketoacyl-synt_C 0.62 43.0 2.72e-01 74.6% 14.1%
3455096 3722.1.1.1 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › MAP65_ASE1 0.62 55.0 3.71e-01 100.0% 29.3%
3868871 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.61 45.0 3.16e-01 81.4% 80.5%
3775067 198.1.1.21 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapA, SapB_2 0.61 43.0 3.45e-01 74.6% 50.0%
3925923 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.61 49.0 4.65e-01 89.8% 98.6%
3657930 3722.1.1.1 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › MAP65_ASE1 0.61 54.0 3.32e-01 100.0% 17.8%
3661393 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.60 50.0 4.81e-01 96.6% 94.3%
4936475 103.4.1.31 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › PF30410 0.60 50.0 4.94e-01 98.3% 95.4%
3308724 3721.1.1.2 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › MAP65_ASE1 0.60 52.0 4.52e-01 98.3% 72.2%
3423943 1128.1.1.2 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR_2 0.59 51.0 4.66e-01 96.6% 82.5%
3811835 7076.1.1.0 ↗ 0.59 47.0 4.61e-01 94.9% 96.9%
4587778 101.1.2.25 ↗ alpha arrays › HTH › HTH › winged helix domain › FUR 0.57 41.0 3.33e-01 79.7% 53.6%
5032465 3567.1.1.194 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer › DUF4234 0.57 47.0 3.26e-01 96.6% 39.1%
4941193 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.56 48.0 4.30e-01 96.6% 81.2%
5060253 632.23.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.56 47.0 4.56e-01 93.2% 95.4%
4956012 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.56 48.0 4.04e-01 98.3% 76.2%
3678817 3722.1.1.1 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › Protein regulator of cytokinesis 1 (PRC1) rod domain › MAP65_ASE1 0.55 45.0 2.94e-01 100.0% 20.3%
4066056 4336.1.1.1 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.54 39.0 3.07e-01 74.6% 75.7%
3926720 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.54 42.0 4.10e-01 86.4% 96.9%
5007277 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.52 40.0 3.65e-01 86.4% 80.0%
3249536 207.1.1.161 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_6, PF29265 0.50 38.0 2.27e-01 84.7% 10.5%